Cyclic Single Atom Vertical Manipulation on a Nonmetallic Surface.

Motivated by the quest for experimental procedures capable of controlled manipulation of single atoms on surfaces, we set up a computational strategy that explores the cyclical vertical manipulation of a broad set of single atoms on the GaAs(110) surface. First-principles simulations of atomic force microscope tip-sample interactions were performed considering families of GaAs and Au-terminated tip apexes with varying crystalline termination. We identified a subset of tips capable of both picking up and depositing an adatom (Ga, As, Al, and Au) any number of times via a modify-restore cycle that "resets" the apex of the scanning probe to its original structure at the end of each cycle. Manipulation becomes successful within a certain window of lateral and vertical tip distances that are observed to be different for extracting and depositing each atom. A practical experimental protocol of special utility for potential cyclical manipulation of single atoms on a nonmetallic surface is proposed.

Externally driven molecular ratchets on a periodic potential surface: a rate equations approach.

The long time dynamics of molecular ratchets on a 1D periodic potential energy surface (PES) subjected to an external stimulus is studied using the rate equation method. The PES consisting of repeated waveforms made of two peaks is considered as an example of a spatially symmetric or asymmetric PES. This PES may, for example, correspond to diffusion of a bipedal molecule that moves along an atomic track via an inchworm walk mechanism [Raval et al., Angew. Chem., Int. Ed., 2015, 54, 7101]. Generalisation to a PES consisting of an arbitrary number of peaks of various heights is straightforward. Assuming the validity of the transition state theory (TST) for the calculation of the transition rates between neighbouring potential wells, the probability of occupying each type of potential well on the PES is obtained analytically, and then the net current for the molecules to move preferentially in a particular direction under application of external fields over a long time is derived. Note that different to methods based on solving numerically the corresponding Fokker-Plank equation, our method is entirely analytical in the limit of weak external fields. The results of the analytical calculations are compared with the exact numerical solution of the derived rate equations. The following external stimuli are considered: constant, sinusoidal and shifted sinusoidal fields due to either a spatially uniform thermal gradient or an electrostatic field. The possible applications of the method for extracting energy from the Brownian motion under load and separating molecules of different chiralities on the surface are also discussed.

Controlling the preferential motion of chiral molecular walkers on a surface.

Molecular walkers standing on two or more "feet" on an anisotropic periodic potential of a crystal surface may perform a one-dimensional Brownian motion at the surface-vacuum interface along a particular direction in which their mobility is the largest. In thermal equilibrium the molecules move with equal probabilities both ways along this direction, as expected from the detailed balance principle, well-known in chemical reactivity and in the theory of molecular motors. For molecules that possess an asymmetric potential energy surface (PES), we propose a generic method based on the application of a time-periodic external stimulus that would enable the molecules to move preferentially in a single direction thereby acting as Brownian ratchets. To illustrate this method, we consider a prototypical synthetic chiral molecular walker, 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using ab initio density functional theory, this molecule moves to the nearest equivalent lattice site via the so-called inchworm mechanism in which it steps first with the rear foot and then with the front foot. As a result, the molecule diffuses via a two-step mechanism, and due to its inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the external stimulus can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed.

Correction: Controlling the preferential motion of chiral molecular walkers on a surface.

[This corrects the article DOI: 10.1039/C9SC01135H.].

The role of isomerization in the kinetics of self-assembly: p-terphenyl-m-dicarbonitrile on the Ag(111) surface.

Using a toolkit of theoretical techniques comprising ab initio density functional theory calculations, the nudged elastic band method and kinetic Monte Carlo (KMC) modeling, we investigate in great detail how para-terphenyl-meta-dicarbonitrile (pTmDC) molecules diffuse and isomerize to self-assemble on the Ag(111) surface. We show that molecules "walk" on the surface via a pivoting mechanism moving each of its two "legs" one at a time. We then identify a peculiar "under-side" isomerization mechanism capable of changing the molecules chirality, and demonstrate that it is fundamental in understanding the growth of hydrogen bonding assembles of ribbons, linkers, clusters and brickwall islands on the Ag(111) surface, as observed in recent scanning tunneling microscopy experiments (ChemPhysChem, 2010, 11, 1446). The discovered underlying atomistic mechanism of self-assembly may be behind the growth of other hydrogen bonding structures of chiral molecules on metal surfaces.